Rarefy: Rarefy a Count Table to Equal Sequencing Depth

In GUniFrac: Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis

Rarefy a Count Table to Equal Sequencing Depth

Description

GUniFrac is also sensitive to different sequencing depth. To compare microbiomes on an equal basis, rarefaction might be used.

Usage

Rarefy(otu.tab, depth = min(rowSums(otu.tab)))

Arguments

otu.tab	OTU count table, row - n sample, column - q OTU
depth	required sequencing depth; If not specified, the lowest sequencing depth is used.

Value

Return a list containing:

otu.tab.rff	rarefied OTU table
discard	IDs of samples that does not reach the specified sequencing depth

Author(s)

Jun Chen <[e-mail]>

References

Chen, J., Bittinger, K., Charlson, E.S., Hoffmann, C., Lewis, J., Wu, G.D., Collman, R.G., Bushman, F.D. and Li, H. (2012). Associating microbiome composition with environmental covariates using generalized UniFrac distances. 28(16): 2106–2113.

Examples

data(throat.otu.tab)
# Rarefaction
otu.tab.rff <- Rarefy(throat.otu.tab, 1024)$otu.tab.rff

GUniFrac documentation built on Sept. 14, 2023, 1:07 a.m.